A thing is right when it tends to preserve the integrity, stability and beauty of the biotic community. It is wrong when it tends otherwise.

Longitudinal study of soils amended with four treatments of varying nutrient availability

Questions:

Are there differences in treatments? Similarities?

  • Differences in community structure as measured by:
    1. Diversity
    2. Richness
    3. Dissimilarity measures (uni-frac + NMDS)
    4. Most abundant species
    5. Differences in replications within a treatment and day…how well does a soil sample of 0.25 get replicated across 12 microcosms?
    6. Soil characteristics? Not sure if focus of this paper should be strongly tied to the chemical measures or not.
    7. Who are the shared OTUs between treatments? Days? Any shared across all?

When do we see these differences?

  • When we see the changes in abundance of a specific OTU for example, can we correlate that with changes in chemical data?
  • Or with a specific day in time?

Who is involed in theses differences?

  • Where do they come from?
  • Do they stick around?

Jared’s thoughts:

  • What is the best way to leverage this data for future work not only on incubation, the STRIPs project for example?
    • Take advantage of longitudinal aspect
    • Representative sequences and FAPROTAX
    • K and N strategists and how are they distributed across treatments and time?
    • Nitrogen cycling bacteria distribution

Objectives for short term:

  1. Use Jin’s rep OTUs to construct a tree
  2. Use uni-frac for ordinations for the paper
  3. Cluster with uni-frac vs. bray-curtis, will capture more information regarding how the OTUs are related.
  4. Include networks in this paper? We could use FAPROTAX to add attributes to the network showing functional information?
From thesis:

In this study, we study the impacts of amendments of both alfalfa and compost, provided at equal rates of total nitrogen, to a soil but with differing C: N ratios chosen to result in immobilization (compost) or mineralization (alfalfa). We characterize both the chemical and microbial response to these amendments and hypothesize that specific microbial communities will respond to initial nitrogen and carbon availability and that this membership will be specific to varying amendments. We expect that these distinct early microbial responders will dominate soil microbial communities in response to organic amendments and will decrease in abundance through time. Our objective was to characterize these early responding microbial communities for various organic amendments and to identify potential microbial membership within organic amendments that may be involved in plant nutrient availability.

Manuscript outline:

  • Introduction
  • Materials and methods
  • Results
  • Discussion/Conclusion

Visualization of results:

Generate list of OTUs from compost and alfalfa amendment:

#p <- readRDS(file = "")